Table 2 Cryo-EM data, model refinement, and validation statistics for apo ECHS1 and ECHS1 in complex with various substrates
ECHS1 apo form | ECHS1–Hexanoyl-CoA | ECHS1–Octanoyl-CoA | ECHS1–Acetoacetyl-CoA | ECHS1–Crotonyl-CoA | |
|---|---|---|---|---|---|
Data collection and processing | |||||
Detector | K3 | K3 | K3 | K3 | K3 |
Magnification | 165,000 | 165,000 | 165,000 | 165,000 | 165,000 |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 50 | 50 | 50 | 50 | 50 |
Defocus range (μM) | −1.0 to −3.0 | −1.0 to −3.0 | −1.0 to −3.0 | −1.0 to −3.0 | −1.0 to −3.0 |
Pixel size (Å) | 0.824 | 0.824 | 0.824 | 0.824 | 0.824 |
Symmetry imposed | D3 | D3 | D3 | D3 | D3 |
Initial particle projections (no.) | 3,200,000 | 3,730,000 | 3,640,000 | 3,600,000 | 3,530,000 |
Final particle projections (no.) | 430,000 | 210,000 | 170,000 | 320,000 | 360,000 |
Map resolution (Å) | 2.18 | 2.55 | 2.29 | 2.27 | 2.23 |
Map resolution range (Å) | 2.50–3.50 | 2.50–3.50 | 2.50–3.50 | 2.50–3.50 | 2.50–3.50 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Model refinement | |||||
Refinement package | PHENIX-1.17.1-3660 | PHENIX-1.17.1-3660 | PHENIX-1.17.1-3660 | PHENIX-1.17.1-3660 | PHENIX-1.17.1-3660 |
Real or reciprocal space | Real space | Real space | Real space | Real space | Real space |
Model-Map CC (mask) | 0.67 | 0.73 | 0.76 | 0.77 | 0.74 |
Model resolution (Å) | 2.64 | 3.14 | 3.02 | 3.03 | 3.06 |
FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
B factors (Å2, min/max/mean value) | |||||
Protein residues | 30.00/94.70/75.72 | 30.00/94.70/75.72 | 30.00/94.70/75.72 | 30.00/94.70/75.72 | 30.00/94.70/75.72 |
Ligand | 87.74/87.74/87.74 | 20.00/87.74/20.41 | 20.00/87.74/20.39 | 20.00/87.74/20.42 | 20.00/87.74/20.42 |
Water | 30.00/30.00/30.00 | 30.00/30.00/30.00 | 30.00/30.00/30.00 | 30.00/30.00/30.00 | 30.00/30.00/30.00 |
Model composition | |||||
Nonhydrogen atoms | 11,834 | 12,164 | 12,176 | 12,158 | 12,152 |
Protein residues | 1560 | 1560 | 1560 | 1560 | 1560 |
R.m.s. deviations | |||||
Bond lengths (Å) | 0.004 | 0.004 | 0.004 | 0.004 | 0.005 |
Bond angles (°) | 0.568 | 0.956 | 0.917 | 0.965 | 1.034 |
Validation | |||||
MolProbity score | 1.44 | 1.33 | 0.90 | 0.94 | 1.32 |
Clashscore | 6.59 | 5.96 | 1.55 | 1.82 | 5.88 |
Rotamer outliers (%) | 1.06 | 0.00 | 0.00 | 0.00 | 0.33 |
Ramachandran plot | |||||
Favored (%) | 97.74 | 98.71 | 98.45 | 99.10 | 98.90 |
Allowed (%) | 2.20 | 1.29 | 1.55 | 0.90 | 1.03 |
Disallowed (%) | 0.06 | 0.00 | 0.00 | 0.00 | 0.07 |
Data availability | |||||
EMDB entry | EMD-60405 | EMD-60406 | EMD-60407 | EMD-60408 | EMD-60409 |
PDB entry | 8ZRU | 8ZRV | 8ZRW | 8ZRX | 8ZRY |
